Shot in the Heart
by SherlockedDancer
Summary: SPOILERS FOR SEASON 3! His Last Vow. Sherlock gets shot, but this time John is there to watch the whole thing. The two of them must discover how to stay safe and find Mary, all while realizing that their feelings for each other may be more than just platonic.
1. Chapter 1

John stood gasping in the doorway as he watched his friend fall to the floor. He couldn't watch this, not again. His best friend had died once and that was already too much for him to bare. He stood frozen unable to grasp anything that was happening. It was almost as if Sherlock was falling in slow motion, his eyes open in surprise. John followed his eyes to where the bullet had come from, the whole scene freezing before him. Saying he was surprised by the person who stood on the other end of the gun would be an understatement. The anger and sadness that rushed in was overwhelming and he continued to stand frozen tears slowly beginning to fall down his face. Suddenly everything was back in motion, John ran to Sherlock, ignoring the pain in his chest as he pushed past his own wife. He pulled out his phone and called for an ambulance, pulling Sherlock into his lap.

"I'm sorry Sherlock, I never meant for things to be like this. She was supposed to be the normal one…"

Tears poured out of his eyes and he did everything he could to keep Sherlock from dying. He continued to feel his pulse and listen to his breathing, fearing the loss of his best friend.

"I'm losing you Sherlock, please, don't do this to me again. Just don't be dead…"

The paramedics rushed in and John followed along as they loaded Sherlock onto a stretcher and put him in an ambulance. He rode along to the hospital and held his friends hand the whole way muttering over and over again,

"I'm sorry Sherlock. I'm so sorry, this shouldn't have happened, this is all my fault."

They arrived at the hospital and rushed Sherlock to an emergency room. John watched from the window as the doctors did everything in their ability to save Sherlock's life. John had never felt something so heart shattering as the sound of Sherlock's pulse stopping, the line going flat and the machine squealing. The doctors all shook their heads in disappointment and started to walk away, cleaning up the room. John couldn't stop himself from bursting into tears. He had lost his best friend, but this time it was real. He stood crying in the window for a few more seconds when he suddenly heard a doctor shouting. He looked up and saw the doctors rushing to Sherlock's bedside. In that moment John witnessed a miracle, he watched as the dead line pulse of his friend began to beep again.

A half hour went by before John was able to enter the room. The doctors wanted to make sure that Sherlock was steady before they left him alone. John walked in and shook hands with the doctor that had saved Sherlock's life.

"Thanks, for everything." John said, smiling at the doctor.

"No problem. Do you happen to be John?" The doctor asked.

"Yeah, why?"

"Well you must be quite some man. The first thing Sherlock said when he woke up was John."

"Oh, well he doesn't have many friends…" I said, surprised myself at Sherlock's first words.

"Oh, well I guess I'll leave you two alone", the doctor said, opening the door to the room for John to enter.

John walked into the white walled room, the sounds of machines and Sherlock's breathing filling the room. He stood next to the bed and smiled down at Sherlock, relieved to see his friend living and breathing.

"Hey Sherlock, how you doing?"

"I'm fine. This whole thing is crazy, they won't let me leave yet."

"Well you did, almost die. Actually technically speaking, you did die."

"So I heard."

They both sat there for a few seconds in silence, unsure of what to say to each other.

"I heard you said my name", John just about whispered.

"Yeah. You were in danger, I decided I shouldn't die."

"Sherlock you can't just decide not to die."

"I did."

"Did not."

"You don't believe me?"

"Not really."

"Well I was just on the edge of death, trying to deal with the pain, but then Moriarty told me you were in danger. I took every last ounce of strength I had left and pulled myself up the staircase."

"What staircase? What Moriarty? Sherlock, what are you talking about?" John just stood confused as to what Sherlock was saying.

"Never mind. All you should know is that I came back to life for you. I guess you could say I was returning the favor."

"What favor?"

"Well you saved my life, so I saved yours."

"I was never in danger Sherlock."

"You do realize your wife is still out there somewhere with a gun."

"Yeah, okay you don't need to remind me."

John stood quiet for a few minutes just staring at Sherlock. His normally pale skin was sickly white, his eyes had dark circles around them, and he looked so fragile, so breakable. John unconsciously reached his hand down and held Sherlock's hand in his own. He sat down in a chair next to the hospital bed and held Sherlock's hand, gently stoking his thumb back and forth, until finally Sherlock fell asleep. John began to fall asleep too, but was awoken by a nurse who had come in to check on Sherlock. She did her business and then left and John decided he better get some sleep in an actual bed. He stood up and bent down, pressing a chaste kiss to Sherlock's forehead before turning and walking out of the room. That night John went to 221B Baker Street where Mrs. Hudson was more than glad to have him back. He started the night in his old bedroom in his old bed but soon felt himself walking to Sherlock's room and laying in Sherlock's bed. He pulled up the covers and inhaled the comforting scent of his best friend.

"I'm sorry Sherlock, this is all my fault. We'll fix it, I promise."


	2. Chapter 2

Sherlock woke up, surprised John wasn't at the hospital yet. 'He must have been really tired', Sherlock thought to himself. After several more hours and still no sign of John, Sherlock began to worry. Sherlock watched the hospital carefully and planned his escape. If John was in danger, he needed to rescue him. After hiding in several utility closets, behind trees, and exiting out the back, Sherlock was able to escape the hospital with nothing but his gown on. He hailed for a cab (which was slightly more difficult than usual) and rode back to Baker Street. As he approached the front door he knew something was wrong. The lock was broken and knocker was straight instead of slightly tilted to the right, someone with OCD then, but not his brother because the foot prints and the finger prints on the door handle were to large, a taller man then. As he entered the flat he knew in an instant who it was, a foul scent filled his senses and his stomach turned as he growled the name,  
"Charles Augustus Magnussen."  
He quickly climbed the staircase and began to slightly panic about John's safety. What he had hurt John? Even worse, what of he had killed him? He did nothing short of kicking down the door and stomping into the room, his eyes quickly falling on Charles, who had made himself comfortable on their couch. Sherlock groaned and searched the room for John, but only saw 2 other men who had accompanied Charles. He didn't take any thought before lashing out,  
"What have you done with John? Where is he? If you lay one finger on him I swear..."  
"Nice to see you too", Charles replied in a calm tone.  
"I'm serious, where is John"  
"I have no idea where your little 'pet' is. Though I'm surprised he's not here, he usually follows you around like a little puppy."  
Sherlock lunged forward and reached his arms out grabbing for Charles neck. His men were quick to stop Sherlock though and they grabbed him holding his arms back and pushing him into a chair.  
"That's really not a good idea Sherlock."  
Sherlock just glared in response and tried to free himself from the death grip of Charles' men.  
"Is the bathroom like the rest of the flat?" Charles asked in disgust.  
"Yes sir." One of the two suites men replied. Charles sighed and walked over to the fire place, unzipped his pants, and began to urinate. Sherlock wrinkled his eyebrows in confusion at the man's odd behavior and sighed.  
"I'm going to ask you one last time, where is John?" Sherlock spat out, through gritted teeth.  
"Once again Sherlock, I don't know where he is and I honestly don't care." The man zipped his pants up on the last word, and turned to face Sherlock.  
"A shame that you trusted Mary, your skills are lacking Sherlock, is this because of sentiment? Weren't you the one who always reminded people that sentiment was a chemical defect found in the losing side? Does that you the loser Sherlock?" With that Charles walked to the door, gesturing for his men to follow. "It was nice seeing you Sherlock, glad to see you're not dead."  
Sherlock walked to the window and watched as the man left the flat and entered a car, driving a way. He walked away from the window and walked to his bedroom, collapsing onto his bed. 'This gunshot wound is really getting in my way', Sherlock thought to himself as he felt the pain begin to overtake his body. As he rolled over he noticed a note lying on the bed. He grabbed it and unfolded it, instantly recognizing Mary's hand writing. His heart stopped for a second but he quickly read the letter.  
_Sherlock,  
I have something that you might want. You owe me, after all I did save your life. Let's meet up, you have my number, call or text me with the location.  
Much love,  
Mary  
_Sherlock whipped out his phone and texted Mary a location and a time quickly pulling himself out of his bed. He changed into some actual clothes and rushed out the door, his eyes welling with the pain from his injury. His injury could wait though, John was in danger and there was no way he could lose the one person he loved. 


	3. Chapter 3

Sherlock arrived at Lauriston Gardens and pulled out his phone, calling Mary. She answered after one ring.  
"Hello Sherlock."  
"Mary."  
"Nice place you have here."  
"You found it then."  
"Not hard to tell a fake apartment when I see one. I'm not exactly blind."  
"I'm standing outside, shall I come in?" It seemed odd Sherlock was asking permission to enter his own territory.  
Mary didn't answer though,  
"John said you were a drama queen, I think I'm a bit of one too."  
With her final words the building lit up with a picture of Sherlock's face.  
How could she have done this so fast?  
"I'm assuming you're wondering how I did this so fast. It was easy really, I planned it a while ago, I know your hiding places."  
Sherlock stayed silent just nodding to himself.  
"I'm waiting for you to come inside", Mary coaxed with a sly voice.  
Sherlock entered the building walking down a dark hallway, stopping halfway down and noticing someone sitting at the other end.  
"So here we are Sherlock. What do you think I should do about you?"  
"Where's John?"  
"Oh I don't know, he's bound to be somewhere."  
"Tell... Me... Where... John... Is", Sherlock growled into the phone. To make his point clear he pulled out his gun and aimed it at the figure sitting in the chair. Suddenly a voice came from behind him,  
"I don't think it's a good idea to shoot."  
Sherlock turned around and found himself face to face with Mary.  
"A dummy... I should have known." Mary just responded with a smirk before pulling out her own gun.  
"I've shot you once, don't make me shoot you again."  
"Mary I need you to listen to me, hear me out."  
"Go on..."  
"I know you and John are...erm... were married, but I don't think your marriage is a good idea anymore. I know you're a good shooter, you could have killed me if you wanted to, but sentiment got the best of you. I think you care about John, but I don't think you love him, and honestly I don't think he could love you after what you have done. You lied, but you lied to protect yourself. I know Charles has information that's life or death to you, but I promise you, if you keep me alive and keep John safe, I can help you. If anyone should know it, it may as well be you, I have loved John from the beginning and I would risk anything for his safety. He can't know though because I know his feelings aren't the same and I can't ruin our relationship. As much as it pains me I can't tell him, but my lovr for John would be fulfilled if you did this for me. Keep John safe, keep me alive, and I save you from Charles."  
Tears trickled down Mary's face and she lowered her gun.  
"Sherlock I'm sorry but it's too late to keep your love for John a secret", and with that she flipped the light switch. Sherlock's face lit up in surprise as he turned around and saw John, sitting at the end of the hallway.


	4. Chapter 4

**Sorry it's been awhile and this chapter is so short… Thanks to everyone who has read, followed, favorite, and reviewed the story, it means a lot to me! –B **

Surprise didn't come close to describing the look on Sherlock's face as he turned around. John sat at the end of the hall, his hair tousled and his eyes looking somewhat like a lost puppy. He was tied to a chair and only sat silently staring back at Sherlock.

"I'm sorry John, please don't be mad. Can we at least stay friends?" Sherlock almost whispered.

"Friends?" John blurted out in complete and utter surprise.

"Is that too much to ask?" Sherlock whined out.

"After everything you said… you just want to be friends?" John asked, slightly gentler than before.

"I'm not sure I follow," Sherlock said in confusion.

"You confess your love, you risk your life to save me, and you only want to be friends? I think you deserve to be a little bit more than friends." John nearly laughed as he said the last few words.

Sherlock turned around to face Mary, now with a more determined look on his face.

"Un-tie John… please."

"Yeah. You promise though? You promise you'll help me?" Mary asked with pleading eyes.

"Of course I'll help you, I know I can trust you", Sherlock answered in a defiant way.

As Mary untied John he couldn't help but blurt out, "Trust her? Really Sherlock? After all she's done…"

"She saved my life." Sherlock said in a matter of fact way.

"She shot you."

"She called an ambulance."

"I called an ambulance."

"She called first. They wouldn't have been there so fast if you were the first to call."

"How would you know?"

John was barely able to finish his sentence as a group of paramedics rushed into the hallway.

"We were told that someone's been shot", one of the paramedics yelled, out of breath.

"That would be me." Sherlock said, raising his hand as he fell to the ground.

John reached out and caught Sherlock, struggling to hold him up.

"God Sherlock, what were you thinking? Leaving the hospital with a gunshot wound, not very smart…"

Sherlock just grunted as John helped hand him over the paramedics. He fell to the ground and they rushed to place an oxygen mask on his face, his skin turning an alarming shade of white. Soon Sherlock was loaded onto a stretcher and into an ambulance, driving off to the hospital. John and Mary stood in an awkward silence for a few minutes before John finally spoke up.

"I think we have a lot to talk about." He was barely able to talk to her without feeling the need to burst into tears.

"Yeah, we should probably go back to Baker Street, tell Mrs. Hudson everything is okay and then talk."

"You have a lot of explaining and a lot of apologizing", John reminded Mary.

She only winced in response and nodded her head as they left the building and took a silent cab ride back to Baker Street.


	5. Chapter 5

After talking to Mrs. Hudson for a moment and explaining that Sherlock was safe and at the hospital, Mary and John headed up the stairs of 221B. Once inside the flat and with the door safely closed John stomped angrily across the room.

"Why? Why do you have to be this way?" John shouted. Obviously exploding with the feelings he had been holding inside.

"John, I'm sorry but it's not completely my fault." Mary answered. Her voice came out soft, and surprisingly innocent.

"What do you mean it's not completely your fault? You're the lying one, the one who shot my best friend." John cringed at the last part.

"Yes John but you chose me. You can't help it. You've always been attracted to dangerous people and dangerous situations. Why do you think you fell in love with Sherlock? Fell in love with me? Have you even realized that your own landlady used to run a drug cartel? You can't help it, you chose these people because you can't stand the ordinary. You could barely stand living in the suburbs with me for a month. You need to be around the city, the crimes, the danger, it's who you are John. You can't completely be mad at me for this because you _chose_ me." As she said the last few words Mary felt a pain shoot there her heart. She had ruined this man. She had fallen in love, gotten married, shot his best friend (no, lover?), and lied.

John stood silently for a few seconds just glaring across the room at Mary. Suddenly he moved, stomping a few steps and then kicking down a table and shouting,

"Why does it always have to be my fault?"

Mary cringed and backed away a few steps, staying silent and giving John some space.

"Okay Mary this is how we're going to do this." He walked across the room and pulled up a chair between his and Sherlock's chairs.

"We're doing it Sherlock's way", he said as he pointed down at the chair. "Always your way", he whispered to an invisible Sherlock. He then sat down in his chair, an army man taking over his facial expression and stature.

Mary crossed the room silently and sat down in the chair, resting her arms in her lap.

"What do you want to know first?" She asked.

"I don't know, just start talking." John wasn't quite sure how much he wanted to know about this women that he thought he knew everything about.

Mary only replied by reaching into her handbag and pulling out a flash drive, the initials A.G.R.A written across it in sharpie.

"What's this?" John said as he reached out and held the flash drive.

"A.G.R.A are the initials of my real name. Everything you need to know about me is on that flash drive. Just don't read it in front of me."

"Why not?" John asked in complete innocence.

"Because if you loved me before, you won't love me after you've read it."

John just nodded his head and slipped the USB in his pocket. Mary spoke up, her voice tinted with fear,

"I'm an intelligence agent. Although my accent is currently English, I can reassure you that it's not my actual accent."

"Oh great, that makes me feel so much better", John responded sarcastically. "So why exactly were you in Charles' office with a gun?"

"Charles is a dangerous man. He knows everything about everyone and he uses the information to ruin people, cities, and governments. People like Charles shouldn't be alive, people like Charles need to be killed."

"Oh great, you're a killer too." John nearly screamed out in frustration.

Mary just looked down silently, tears forming in her eyes.

"I think I'm going to head over to the hospital to visit Sherlock, it's probably best you went home. Don't bother calling, I'll contact you when I'm ready too." John stood up with his final words and gestured to the door.

Mary slowly stood up, looking John in the eyes. Her eyes searched the man in front of her but she was only met with his military glare. The tears in her eyes welled up even more as she turned to leave the flat. John held the door open,

"Goodbye Mary."

"Goodbye John."

Both their goodbyes meant more than just Mary leaving the flat. It was goodbye to all the lies that had been told, all the secrets that had been kept, and all the love that there had ever been between the two. As John closed the door he turned and pressed his back against it, sliding down to the floor. He rested his head on his knees and put his hands on his head. Why had he ever let this happen? What would he do now? The past two years of his life had been a lie and there was nothing he could do to fix what had been done. In that moment, as he felt the tears flow freely from his eyes, John realized how much he needed Sherlock. Sherlock was always there for him, always protected him, always made him smile, and most of all, always loved him. He needed Sherlock. And as he said goodbye to the lie he and Mary had been living, he said hello to the new life that he would live with Sherlock.


	6. Chapter 6

Sorry it's been awhile since I've updated. If you guys want me to keep going with the story I would more than willingly continue posting and adding on new chapters. Let me know what you think. Anywho I will try to post a new chapter soon. 


	7. Chapter 7

**Sorry it's so short but I was just so happy that you all liked it and wanted me to continue so I decided that I should give you guys a little something -B**

Sherlock lay in the all too familiar hospital bed, only listening to the steady sound of his heart rate monitor over and over again,

"Beep…beep…beep"

This place was far too boring and there wasn't nearly enough crimes to solve. Sherlock was left alone with his thoughts and at this moment in time there were three people on his mind; John, Mary, and Charles Augustus Magnussen. Christmas was in less than a week and Sherlock knew that he had to meet up with Charles soon. Although Mary had almost killed him, he knew her reasons why and he had promised he would help her. Suddenly Sherlock was pulled out of his thoughts by a knock on the door.

"Someone is here to see you Mr. Holmes", a nurse informed.

"Bring them in."

Sherlock suddenly felt the air go cold and he could have sworn his heart had skipped a beat, if there had not been a heart monitor telling him otherwise.

"How's hospital life?" The cold and icy voice asked.

"Boring." Sherlock kept a straight face and a calm demeanor as he answered the icy man.

"Yeah it's a shame. Not many criminals here."

"So pressure points is it? You sit there and find people's pressure points and use them to bring them down." Sherlock said the words in a more of a matter of fact way rather than as a question. Charles responded with only a smile. "You can read people. You have files hidden in a vault with all their personal information and you save it into those." And with that Sherlock reached across and grabbed Charles glasses.

Charles watched in amusement as Sherlock slipped on the glasses. There was a moment of silence and then,

"Nothing." Sherlock's face filled with confusion as he slipped the glasses off. "Just regular spectacles", he said as he handed back the glasses.

"It appears so Mr. Holmes. Although I would love to show you the vaults sometime. You and your little pet… John."

"Leave John out of this. He's done nothing."

"Yes but his wife is quite the lady isn't she. I think we can agree that if you bring me what I want I'll show you my vaults, and that includes John."

Sherlock thought for a moment before finally responding,

"Fine. Can't wait to spend Christmas with you."

Charles stood and began to walk out of the room,

"I'm looking forward to your company." And with that he was gone.


End file.
